Use of a combined ex vivo/in vivo population approach for screening of human genes involved in the human immunodeficiency virus type 1 life cycle for variants influencing disease progression.

Humans differ substantially with respect to susceptibility to human immunodeficiency virus type 1 (HIV-1). We evaluated variants of nine host genes participating in the viral life cycle for their role in modulating HIV-1 infection. Alleles were assessed ex vivo for their impact on viral replication in purified CD4 T cells from healthy blood donors (n = 128). Thereafter, candidate alleles were assessed in vivo in a cohort of HIV-1-infected individuals (n = 851) not receiving potent antiretroviral therapy. As a benchmark test, we tested 12 previously reported host genetic variants influencing HIV-1 infection as well as single nucleotide polymorphisms in the nine candidate genes. This led to the proposition of three alleles of PML, TSG101, and PPIA as potentially associated with differences in progression of HIV-1 disease. In a model considering the combined effects of new and previously reported gene variants, we estimated that their effect might be responsible for lengthening or shortening by up to 2.8 years the period from 500 CD4 T cells/mul to <200 CD4 T cells/mul.

Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data.

BACKGROUND: Prognosis prediction for resected primary colon cancer is based on the T-stage Node Metastasis (TNM) staging system. We investigated if four well-documented gene expression risk scores can improve patient stratification. METHODS: Microarray-based versions of risk-scores were applied to a large independent cohort of 688 stage II/III tumors from the PETACC-3 trial. Prognostic value for relapse-free survival (RFS), survival after relapse (SAR), and overall survival (OS) was assessed by regression analysis. To assess improvement over a reference, prognostic model was assessed with the area under curve (AUC) of receiver operating characteristic (ROC) curves. All statistical tests were two-sided, except the AUC increase. RESULTS: All four risk scores (RSs) showed a statistically significant association (single-test, P < .0167) with OS or RFS in univariate models, but with HRs below 1.38 per interquartile range. Three scores were predictors of shorter RFS, one of shorter SAR. Each RS could only marginally improve an RFS or OS model with the known factors T-stage, N-stage, and microsatellite instability (MSI) status (AUC gains < 0.025 units). The pairwise interscore discordance was never high (maximal Spearman correlation = 0.563) A combined score showed a trend to higher prognostic value and higher AUC increase for OS (HR = 1.74, 95% confidence interval [CI] = 1.44 to 2.10, P < .001, AUC from 0.6918 to 0.7321) and RFS (HR = 1.56, 95% CI = 1.33 to 1.84, P < .001, AUC from 0.6723 to 0.6945) than any single score. CONCLUSIONS: The four tested gene expression-based risk scores provide prognostic information but contribute only marginally to improving models based on established risk factors. A combination of the risk scores might provide more robust information. Predictors of RFS and SAR might need to be different.

Structural quality of soils cultivated with coffee and pasture in an environmental protection area

Studies of soils in Environmental Protection Areas (EPAs) are of great importance, because they are an essential component of ecosystems, directly interfering in environmental sustainability. The objective of this study was to evaluate the structural quality of soil cultivated with coffee and used as pasture in the Capituva's River microbasin, which is located in the Environmental Protection Area in Coqueiral, south of the state of Minas Gerais. Uniaxial compression test (preconsolidation test) and soil resistance to penetration were used. Undisturbed samples were taken from the surface layer (0-5 cm) of the soils in the area: a typic dystrophic Red Latosol (LVd - Oxisol), a typic eutrophic Red Argisol (PVe - Ultisol), and a typic dystrophic Haplic Cambisol (CXbd - Inceptisol). A significant linear positive correlation was observed between the results of the preconsolidation test and soil resistance to penetration. Load bearing capacity of soil could be estimated accordingly by means of penetration resistance for LVd, PVe, and CXbd. Cambisol - CXbd showed lower loading support capacity and resistance to penetration than LVd and PVe, due to the better crop management in this soil that resulted in higher physical quality which accounts for higher production and environmental sustainability.

Combinations of prognostic tools for identification of high-risk normotensive patients with acute symptomatic pulmonary embolism.

Background: In haemodynamically stable patients with acute symptomatic pulmonary embolism (PE), studies have not evaluated the usefulness of combining the measurement of cardiac troponin, transthoracic echocardiogram (TTE), and lower extremity complete compression ultrasound (CCUS) testing for predicting the risk of PE-related death. Methods: The study assessed the ability of three diagnostic tests (cardiac troponin I (cTnI), echocardiogram, and CCUS) to prognosticate the primary outcome of PE-related mortality during 30 days of follow-up after a diagnosis of PE by objective testing. Results: Of 591 normotensive patients diagnosed with PE, the primary outcome occurred in 37 patients (6.3%; 95% CI 4.3% to 8.2%). Patients with right ventricular dysfunction (RVD) by TTE and concomitant deep vein thrombosis (DVT) by CCUS had a PE-related mortality of 19.6%, compared with 17.1% of patients with elevated cTnI and concomitant DVT and 15.2% of patients with elevated cTnI and RVD. The use of any two-test strategy had a higher specificity and positive predictive value compared with the use of any test by itself. A combined three-test strategy did not further improve prognostication. For a subgroup analysis of high-risk patients, according to the pulmonary embolism severity index (classes IV and V), positive predictive values of the two-test strategies for PE-related mortality were 25.0%, 24.4% and 20.7%, respectively. Conclusions: In haemodynamically stable patients with acute symptomatic PE, a combination of echocardiography (or troponin testing) and CCUS improved prognostication compared with the use of any test by itself for the identification of those at high risk of PE-related death.

Repeated sprinting on natural grass impairs vertical stiffness but does not alter plantar loading in soccer players.

This study aimed to determine changes in spring-mass model (SMM) characteristics, plantar pressures, and muscle activity induced by the repetition of sprints in soccer-specific conditions; i.e., on natural grass with soccer shoes. Thirteen soccer players performed 6 × 20 m sprints interspersed with 20 s of passive recovery. Plantar pressure distribution was recorded via an insole pressure recorder device divided into nine areas for analysis. Stride temporal parameters allowed to estimate SMM characteristics. Surface electromyographic activity was monitored for vastus lateralis, rectus femoris, and biceps femoris muscles. Sprint time, contact time, and total stride duration lengthened from the first to the last repetition (+6.7, +12.9, and +9.3%; all P < 0.05), while flight time, swing time, and stride length remained constant. Stride frequency decrease across repetitions approached significance (-6.8%; P = 0.07). No main effect of the sprint number or any significant interaction between sprint number and foot region was found for maximal force, mean force, peak pressure and mean pressure (all P > 0.05). Center of mass vertical displacement increased (P < 0.01) with time, together with unchanged (both P > 0.05) peak vertical force and leg compression. Vertical stiffness decreased (-15.9%; P < 0.05) across trials, whereas leg stiffness changes were not significant (-5.9%; P > 0.05). Changes in root mean square activity of the three tested muscles over sprint repetitions were not significant. Although repeated sprinting on natural grass with players wearing soccer boots impairs their leg-spring behavior (vertical stiffness), there is no substantial concomitant alterations in muscle activation levels or plantar pressure patterns.

Evaluation of Hot Mix Asphalt Moisture Sensitivity Using the Nottingham Asphalt Test Equipment, July 2005

Moisture sensitivity of Hot Mix Asphalt (HMA) mixtures, generally called stripping, is a major form of distress in asphalt concrete pavement. It is characterized by the loss of adhesive bond between the asphalt binder and the aggregate (a failure of the bonding of the binder to the aggregate) or by a softening of the cohesive bonds within the asphalt binder (a failure within the binder itself), both of which are due to the action of loading under traffic in the presence of moisture. The evaluation of HMA moisture sensitivity has been divided into two categories: visual inspection test and mechanical test. However, most of them have been developed in pre-Superpave mix design. This research was undertaken to develop a protocol for evaluating the moisture sensitivity potential of HMA mixtures using the Nottingham Asphalt Tester (NAT). The mechanisms of HMA moisture sensitivity were reviewed and the test protocols using the NAT were developed. Different types of blends as moisture-sensitive groups and non-moisture-sensitive groups were used to evaluate the potential of the proposed test. The test results were analyzed with three parameters based on performance character: the retained flow number depending on critical permanent deformation failure (RFNP), the retained flow number depending on cohesion failure (RFNC), and energy ratio (ER). Analysis based on energy ratio of elastic strain (EREE ) at flow number of cohesion failure (FNC) has higher potential to evaluate the HMA moisture sensitivity than other parameters. If the measurement error in data-acquisition process is removed, analyses based on RFNP and RFNC would also have high potential to evaluate the HMA moisture sensitivity. The vacuum pressure saturation used in AASHTO T 283 and proposed test has a risk to damage specimen before the load applying.

Changes in leg spring behaviour, plantar loading and foot mobility magnitude induced by an exhaustive treadmill run in adolescent middle-distance runners.

OBJECTIVES: This study aimed to determine adjustments in spring-mass model characteristics, plantar loading and foot mobility induced by an exhaustive run. DESIGN: Within-participants repeated measures. METHODS: Eleven highly-trained adolescent middle-distance runners ran to exhaustion on a treadmill at a constant velocity corresponding to 95% of velocity associated with VO₂max (17.8 ± 1.4 kmh(-1), time to exhaustion=8.8 ± 3.4 min). Contact time obtained from plantar pressure sensors was used to estimate spring-mass model characteristics, which were recorded (during 30 s) 1 min after the start and prior to exhaustion using pressure insoles. Foot mobility magnitude (a composite measure of vertical and medial-lateral mobility of the midfoot) was measured before and after the run. RESULTS: Mean contact area (foot to ground), contact time, peak vertical ground reaction force, centre of mass vertical displacement and leg compression increased significantly with fatigue, while flight time, leg stiffness and mean pressure decreased. Leg stiffness decreased because leg compression increased to a larger extent than peak vertical ground reaction forces. Step length, step frequency and foot mobility magnitude did not change at exhaustion. CONCLUSIONS: The stride pattern of adolescents when running on a treadmill at high constant velocity deteriorates near exhaustion, as evidenced by impaired leg-spring behaviour (leg stiffness) and altered plantar loading.

Laboratory Performance Evaluation of CIR-Emulsion and it Comparison Against CIR-Form Test Result from Phase II, Final Report TR-578 Phase III, December 2009

Currently, no standard mix design procedure is available for CIR-emulsion in Iowa. The CIR-foam mix design process developed during the previous phase is applied for CIR-emulsion mixtures with varying emulsified asphalt contents. Dynamic modulus test, dynamic creep test, static creep test and raveling test were conducted to evaluate the short- and long-term performance of CIR-emulsion mixtures at various testing temperatures and loading conditions. A potential benefit of this research is a better understanding of CIR-emulsion material properties in comparison with those of CIR-foam material that would allow for the selection of the most appropriate CIR technology and the type and amount of the optimum stabilization material. Dynamic modulus, flow number and flow time of CIR-emulsion mixtures using CSS-h were generally higher than those of HFMS-2p. Flow number and flow time of CIR-emulsion using RAP materials from Story County was higher than those from Clayton County. Flow number and flow time of CIR-emulsion with 0.5% emulsified asphalt was higher than CIR-emulsion with 1.0% or 1.5%. Raveling loss of CIR-emulsion with 1.5% emulsified was significantly less than those with 0.5% and 1.0%. Test results in terms of dynamic modulus, flow number, flow time and raveling loss of CIR-foam mixtures are generally better than those of CIR-emulsion mixtures. Given the limited RAP sources used for this study, it is recommended that the CIR-emulsion mix design procedure should be validated against several RAP sources and emulsion types.

Diagnosis of pulmonary embolism by multidetector CT alone or combined with venous ultrasonography of the leg: a randomised non-inferiority trial.

BACKGROUND: Multislice CT (MSCT) combined with D-dimer measurement can safely exclude pulmonary embolism in patients with a low or intermediate clinical probability of this disease. We compared this combination with a strategy in which both a negative venous ultrasonography of the leg and MSCT were needed to exclude pulmonary embolism. METHODS: We included 1819 consecutive outpatients with clinically suspected pulmonary embolism in a multicentre non-inferiority randomised controlled trial comparing two strategies: clinical probability assessment and either D-dimer measurement and MSCT (DD-CT strategy [n=903]) or D-dimer measurement, venous compression ultrasonography of the leg, and MSCT (DD-US-CT strategy [n=916]). Randomisation was by computer-generated blocks with stratification according to centre. Patients with a high clinical probability according to the revised Geneva score and a negative work-up for pulmonary embolism were further investigated in both groups. The primary outcome was the 3-month thromboembolic risk in patients who were left untreated on the basis of the exclusion of pulmonary embolism by diagnostic strategy. Clinicians assessing outcome were blinded to group assignment. Analysis was per protocol. This study is registered with ClinicalTrials.gov, number NCT00117169. FINDINGS: The prevalence of pulmonary embolism was 20.6% in both groups (189 cases in DD-US-CT group and 186 in DD-CT group). We analysed 855 patients in the DD-US-CT group and 838 in the DD-CT group per protocol. The 3-month thromboembolic risk was 0.3% (95% CI 0.1-1.1) in the DD-US-CT group and 0.3% (0.1-1.2) in the DD-CT group (difference 0.0% [-0.9 to 0.8]). In the DD-US-CT group, ultrasonography showed a deep-venous thrombosis in 53 (9% [7-12]) of 574 patients, and thus MSCT was not undertaken. INTERPRETATION: The strategy combining D-dimer and MSCT is as safe as the strategy using D-dimer followed by venous compression ultrasonography of the leg and MSCT for exclusion of pulmonary embolism. An ultrasound could be of use in patients with a contraindication to CT.

Innovative Solutions for Slope Stability Reinforcement and Characterization: Vol. I, TR-489, 2005

Soil slope instability concerning highway infrastructure is an ongoing problem in Iowa, as slope failures endanger public safety and continue to result in costly repair work. Characterization of slope failures is complicated, because the factors affecting slope stability can be difficult to discern and measure, particularly soil shear strength parameters. While in the past extensive research has been conducted on slope stability investigations and analysis, this research consists of field investigations addressing both the characterization and reinforcement of such slope failures. The current research focuses on applying an infrequently-used testing technique comprised of the Borehole Shear Test (BST). This in-situ test rapidly provides effective (i.e., drained) shear strength parameter values of soil. Using the BST device, fifteen Iowa slopes (fourteen failures and one proposed slope) were investigated and documented. Particular attention was paid to highly weathered shale and glacial till soil deposits, which have both been associated with slope failures in the southern Iowa drift region. Conventional laboratory tests including direct shear tests, triaxial compression tests, and ring shear tests were also performed on undisturbed and reconstituted soil samples to supplement BST results. The shear strength measurements were incorporated into complete evaluations of slope stability using both limit equilibrium and probabilistic analyses. The research methods and findings of these investigations are summarized in Volume 1 of this report. Research details of the independent characterization and reinforcement investigations are provided in Volumes 2 and 3, respectively. Combined, the field investigations offer guidance on identifying the factors that affect slope stability at a particular location and also on designing slope reinforcement using pile elements for cases where remedial measures are necessary. The research findings are expected to benefit civil and geotechnical engineers of government transportation agencies, consultants, and contractors dealing with slope stability, slope remediation, and geotechnical testing in Iowa.

Pile Design and Tests for Integral Abutment Bridges, HR-273, 1987

Expansion joints increase both the initial cost and the maintenance cost of bridges. Integral abutment bridges provide an attractive design alternative because expansion joints are eliminated from the bridge itself. However, the piles in these bridges are subjected to horizontal movement as the bridge expands and contracts during temperature changes. The objective of this research was to develop a method of designing piles for these conditions. Separate field tests simulating a pile and a bridge girder were conducted for three loading cases: (1) vertical load only, (2) horizontal displacement of pile head only, and (3) combined horizontal displacement of pile head with subsequent vertical load. Both tests (1) and (3) reached the same ultimate vertical load, that is, the horizontal displacement had no effect on the vertical load capacity. Several model tests were conducted in sand with a scale factor of about 1:10. Experimental results from both the field and model tests were used to develop the vertical and horizontal load-displacement properties of the soil. These properties were input into the finite element computer program Integral Abutment Bridge Two-Dimensional (IAB2D), which was developed under a previous research contract. Experimental and analytical results compared well for the test cases. Two alternative design methods, both based upon the American Association of State Highway and Transportation Officials (AASHTO) Specification, were developed. Alternative One is quite conservative relative to IAB2D results and does not permit plastic redistribution of forces. Alternative Two is also conservative when compared to IAB2D, but plastic redistribution is permitted. To use Alternative Two, the pile cross section must have sufficient inelastic rotation capacity before local buckling occurs. A design example for a friction pile and an end-bearing pile illustrates both alternatives.

Surgical outcomes of Baerveldt aqueous shunt implantation versus combined phacoemulsification and Baerveldt aqueous shunt implantation

Purpose: To examine the efficacy and safety of Baerveldt shunt (BS) implantation compared to combined phacoemulsification and Baerveldt shunt implantation (PBS). This study was designed to detect a difference in IOP reduction of 20% (~4mmHg) between groups with 90% power. Methods: Sixty patients with medically uncontrolled glaucoma, prospectively underwent either or BS implantation with phacoemulsification (Group PBS; n=30) or BS implantation alone (group BS; n=30, pseudophakic eyes only). Groups were matched for age, glaucoma subtype and length of follow-up. Pre and post-operative measures recorded included patient demographics, visual acuity, IOP, number of glaucoma medications (GMs) and all complications. Success was defined as IOP≤21mmHg and 20% reduction in IOP from baseline with or without GMs. Results: Age of PBS and BS groups was 61 vs 62 years respectively (p=0.72*). There were no significant differences in preoperative baseline characteristics: PBS vs PB, mean IOP =25.5mmHg (standard deviation (SD); ±10.3mmHg) vs 26.1mmHg (SD ±10.6mmHg), p=0.81*; mean GMs=3.0 (SD ±1.1) vs 3.1 (SD ±1.0), p=0.83*; mean VA=0.3 vs 0.3, p=0.89*. At year one there were no significant differences observed between groups in post-operative IOP, GMs or VA, mean IOP =14.1mmHg (SD ±5.4mmHg) vs 11.5 mmHg (SD ±4.2mmHg), p=0.12*; mean GMs=1.6 (SD ±1.4) vs 1.1 (SD ±1.1), p=0.23*; mean VA=0.5 vs 0.4, p=0.46*. Complication rates were similar between the two groups (7% vs 14%). Success rate was lower in eyes with PBS (71%) than with BS (88%), however this did not reach statistical significance (p=0.95, log-rank test). * two-sample t-test Conclusions: There were no significant differences at year one in success or complication rates between PBS and BS groups suggesting that simultaneous phacoemulsification does not have a marked (difference of >4mmHg) effect on tube function. IOP reduction and success were less in the PBS group, a larger sample (n=120) would be required to investigate if there is a 10% difference in IOP reduction between groups, however it is unclear if this would be a clinically significant difference to justify separate surgeries.

Preventing Cracking at Diaphragm/Plate Girder Connections in Steel Bridges, HR-393, 1998

Some of the Iowa Department of Transportation (Iowa DOT) continuous, steel, welded plate girder bridges have developed web cracking in the negative moment regions at the diaphragm connection plates. The cracks are due to out-of-plane bending of the web near the top flange of the girder. The out-of-plane bending occurs in the "web-gap", which is the portion of the girder web between (1) the top of the fillet welds attaching the diaphragm connection plate to the web and (2) the fillet welds attaching the flange to the web. A literature search indicated that four retrofit techniques have been suggested by other researchers to prevent or control this type of cracking. To eliminate the problem in new bridges, AASHTO specifications require a positive attachment between the connection plate and the top (tension) flange. Applying this requirement to existing bridges is expensive and difficult. The Iowa DOT has relied primarily on the hole-drilling technique to prevent crack extension once cracking has occurred; however, the literature indicates that hole-drilling alone may not be entirely effective in preventing crack extension. The objective of this research was to investigate experimentally a method proposed by the Iowa DOT to prevent cracking at the diaphragm/plate girder connection in steel bridges with X-type or K-type diaphragms. The method consists of loosening the bolts at some connections between the diaphragm diagonals and the connection plates. The investigation included selecting and testing five bridges: three with X-type diaphragms and two with K-type diaphragms. During 1996 and 1997, these bridges were instrumented using strain gages and displacement transducers to obtain the response at various locations before and after implementing the method. Bridges were subjected to loaded test trucks traveling in different lanes with speeds varying from crawl speed to 65 mph (104 km/h) to determine the effectiveness of the proposed method. The results of the study show that the effect of out-of-plane loading was confined to widths of approximately 4 in. (100 mm) on either side of the connection plates. Further, they demonstrate that the stresses in gaps with drilled holes were higher than those in gaps without cracks, implying that the drilling hole technique is not sufficient to prevent crack extension. The behavior of the web gaps in X-type diaphragm bridges was greatly enhanced by the proposed method as the stress range and out-of-plane distortion were reduced by at least 42% at the exterior girders. For bridges with K-type diaphragms, a similar trend was obtained. However, the stress range increased in one of the web gaps after implementing the proposed method. Other design aspects (wind, stability of compression flange, and lateral distribution of loads) must be considered when deciding whether to adopt the proposed method. Considering the results of this investigation, the proposed method can be implemented for X-type diaphragm bridges. Further research is recommended for K-type diaphragm bridges.

Combined Serum Creatinine and Cystatin C Schwartz Formula Predicts Kidney Function Better than the Combined CKD-EPI Formula in Children.

Background: The combined serum creatinine (SCreat) and cystatin C (CysC) CKD-EPI formula constitutes a new advance for glomerular filtration rate (GFR) estimation in adults. Using inulin clearances (iGFRs), the revised SCreat and the combined Schwartz formulas, this study aims to evaluate the applicability of the combined CKD-EPI formula in children. Method: 201 iGFRs for 201 children were analyzed and divided by chronic kidney disease (CKD) stages (iGFRs ≥90 ml/min/1.73 m(2), 90 > iGFRs > 60, and iGFRs ≤59), and by age groups (<10, 10-15, and >15 years). Medians with 95% confidence intervals of bias, precision, and accuracies within 30% of the iGFRs, for all three formulas, were compared using the Wilcoxon signed-rank test. Results: For the entire cohort and for all CKD and age groups, medians of bias for the CKD-EPI formula were significantly higher (p < 0.001) and precision was significantly lower than the solely SCreat and the combined SCreat and CysC Schwartz formulas. We also found that using the CKD-EPI formula, bias decreased and accuracy increased while the child age group increased, with a better formula performance above 15 years of age. However, the CKD-EPI formula accuracy is 58% compared to 93 and 92% for the SCreat and combined Schwartz formulas in this adolescent group. Conclusions: The performance of the combined CKD-EPI formula improves in adolescence compared with younger ages. Nevertheless, the CKD-EPI formula performs more poorly than the SCreat and the combined Schwartz formula in pediatric population. © 2013 S. Karger AG, Basel.

Laboratory Performance Evaluation of CIR-Emulsion and its Comparison Against CIR-Foam Test Results from Phase 2, TR-474, 2009

Currently, no standard mix design procedure is available for CIR-emulsion in Iowa. The CIR-foam mix design process developed during the previous phase is applied for CIR-emulsion mixtures with varying emulsified asphalt contents. Dynamic modulus test, dynamic creep test, static creep test and raveling test were conducted to evaluate the short- and long-term performance of CIR-emulsion mixtures at various testing temperatures and loading conditions. A potential benefit of this research is a better understanding of CIR-emulsion material properties in comparison with those of CIR-foam material that would allow for the selection of the most appropriate CIR technology and the type and amount of the optimum stabilization material. Dynamic modulus, flow number and flow time of CIR-emulsion mixtures using CSS- 1h were generally higher than those of HFMS-2p. Flow number and flow time of CIR-emulsion using RAP materials from Story County was higher than those from Clayton County. Flow number and flow time of CIR-emulsion with 0.5% emulsified asphalt was higher than CIR-emulsion with 1.0% or 1.5%. Raveling loss of CIR-emulsion with 1.5% emulsified was significantly less than those with 0.5% and 1.0%. Test results in terms of dynamic modulus, flow number, flow time and raveling loss of CIR-foam mixtures are generally better than those of CIR-emulsion mixtures. Given the limited RAP sources used for this study, it is recommended that the CIR-emulsion mix design procedure should be validated against several RAP sources and emulsion types.